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Afternoon becomes an evening when the sun starts to set. An evening becomes a night when the sun is fully set.

"I was up at two this morning" has several implied meanings. One of them equals to "I was up until two last night", others do not.

If you were up until two last night, you might legitimately express that with "I was up at two this morning". But if you were up at two this morning, saying "I was up until two last night" might or might not convey the truth. For example, you might have just gotten up.

Many if not all languages have nuances like this. I don't find them particularly odd at all, or specific to English, for that matter...